There isn't a way to undo it that I know of.
You're not doing anything irrevocable when you do online check-in. It doesn't commit you to the reservation, assign you to a room, or initiate any charges. It's just a convenience; a way to enter a credit card number and a generic request if you choose to.
If you cancel your reservation, when the reservation is removed from the system the online check-in goes with it.